Hello,
In iOS 5.0, Apple introduced a new system level function that would free up "disk" space if the OS found that there was limited or zero free space on the device.
The OS would then run through the apps, possibly ordered by apps with the largest amount of data and try and purge anything from the Documents folder of that app (Documents being where apps should store any data files. It's the folder you see when you view the "File Sharing" section of an app in iTunes)
Originally there wasn't a way to prevent this, and developers complained about this, as there should be some way for developers to protect the data that users are downloaded from the OS being able to just wipe it out.
This was changed and developers were able to flag a file so it would not be deleted by the OS.
We introduced an option in the settings for the app (as found by going into the Settings app, and then selecting the Kobo item) to allow you to specify how many books were permanently stored. The options are:
All Items
10 Most Recent Items
5 Most Recent Items
My Current Read
No Items
I believe the original implementation had 5 Most Recent Items as the default, but it was changed in later versions to All Items, and that is how it remains, so all your books should be kept.
What this means is that when the OS detects low, or no space left, it will look at the app and realize that the files in there are flagged to not be deleted and it leaves them alone.
I haven't seen books removed by this method unless the option isn't set to All Items. The app does not remove the books either, it's the OS itself that does it.
The only thing I could think of is that the option might not be reporting back it's actual setting, for example, you had the version of the app where this functionality was put it and it was set to "5 most recent items", and through upgrades of the app, it never got updated to the "All Items" option, even though the settings display that as being the default. Therefore, if the free space was low enough, the books could be removed.
What you could try is going into the settings app, then the Kobo item and then Permanently Store option, and toggle it from whatever it is currently configured to use to another option, then set it back to All Items. This should enforce that all books are going to be prevented from deletion.
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